Professor Turnell's flight touched down on Friday morning at Melbourne Airport, where he was reunited with his wife Ha Vu.
He left Bangkok late on Thursday evening before getting an overnight flight following his surprise release.
Prof Turnell was arrested in early 2021 after Myanmar's military junta seized power and was sentenced to three years' jail in September for "violating the country's official state secrets act".
Ha Vu said on Friday she was thankful to everyone who advocated for his release, including Foreign Minister Penny Wong and others in the Australian government.
"I am overwhelmed with joy at the news that my beloved husband, Sean, is coming home," she said in a statement.
"After nearly 22 months apart, our priority right now is to spend time together as a family."
Foreign Minister Penny Wong said she spoke to Prof Turnell after he landed in Bangkok and described him as being in very good spirits.
"His return will be an enormous relief to his wife Ha Vu and to all of his friends and supporters here in Australia and overseas," she told reporters in Adelaide.
"Ha Vu has been a tower of strength through this ordeal and I wish both she and Sean well for this reunion and time together."
Prof Turnell was freed earlier on Thursday under an amnesty covering close to 6000 prisoners to celebrate Myanmar's National Victory Day.
Prime Minister Anthony Albanese, in Bangkok for the APEC summit, spoke to the 58-year-old over the phone and said he was in "amazingly good spirits".
Prof Turnell, who lives in Mr Albanese's electorate, was even making jokes and apologised for not voting in the election.
Mr Albanese reassured him he would not be fined.
Prof Turnell also told Mr Albanese "people have been wonderful" and wanted to thank Australians for their support.
"He's a remarkable man and he was (in Myanmar) doing his job as an economic policy adviser - nothing more, nothing less," Mr Albanese told reporters.
Prof Turnell told Mr Albanese the Australian embassy in Myanmar dropped off food hampers in tote bags emblazoned with the Australian crest while he was in jail.
"He would put the tote bags where the bars were on the cell ... so both he and the guards who were detaining him could see the Australian crest and he could keep that optimism," Mr Albanese said.
"The Australian crest, of course, with the kangaroo and emu that don't go backwards."
The prime minister thanked leaders of ASEAN nations for their advocacy and asked for Prof Turnell's privacy to be respected upon his return home.
Prof Turnell was working as an adviser to ousted Myanmar leader Aung San Suu Kyi when he was arrested in 2021 after the military seized power in a coup.
He has continuously denied he committed any crime and Australian officials and media were locked out of his trial.
Amnesty International Australia director Tim O'Connor said Myanmar's military rule had repeatedly jailed innocent people.
Prof Turnell was one of four international prisoners freed on Thursday, including Japanese filmmaker Toru Kubota, ex-British diplomat Vicky Bowman and American Kyaw Htay Oo.
ASEAN Parliamentarians for Human Rights said it was important to remember thousands of political prisoners remained in the country's jails.
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